Implementation of the GVP-Transformer, which was used in the paper "Learning inverse folding from millions of predicted structures" for de novo protein design alongside Alphafold2

Overview

GVP Transformer (wip)

Implementation of the GVP-Transformer, which was used in the paper Learning inverse folding from millions of predicted structures for de novo protein design alongside Alphafold2. The base neural network consists of an invariant geometric network, GVP, combined with an encoder / decoder transformer.

It will also offer the tools for enabling autoregressive infilling

Citations

@article {Hsu2022.04.10.487779,
    author  = {Hsu, Chloe and Verkuil, Robert and Liu, Jason and Lin, Zeming and Hie, Brian and Sercu, Tom and Lerer, Adam and Rives, Alexander},
    title   = {Learning inverse folding from millions of predicted structures},
    elocation-id = {2022.04.10.487779},
    year    = {2022},
    doi     = {10.1101/2022.04.10.487779},
    publisher = {Cold Spring Harbor Laboratory},
    URL     = {https://www.biorxiv.org/content/early/2022/04/10/2022.04.10.487779},
    eprint  = {https://www.biorxiv.org/content/early/2022/04/10/2022.04.10.487779.full.pdf},
    journal = {bioRxiv}
}
Owner
Phil Wang
Working with Attention. It's all we need
Phil Wang
Official Implementation of VAT

Semantic correspondence Few-shot segmentation Cost Aggregation Is All You Need for Few-Shot Segmentation For more information, check out project [Proj

Hamacojr 114 Dec 27, 2022
Source code for paper "Deep Diffusion Models for Robust Channel Estimation", TBA.

diffusion-channels Source code for paper "Deep Diffusion Models for Robust Channel Estimation". Generic flow: Use 'matlab/main.mat' to generate traini

The University of Texas Computational Sensing and Imaging Lab 15 Dec 22, 2022
Weakly Supervised Dense Event Captioning in Videos, i.e. generating multiple sentence descriptions for a video in a weakly-supervised manner.

WSDEC This is the official repo for our NeurIPS paper Weakly Supervised Dense Event Captioning in Videos. Description Repo directories ./: global conf

Melon(Xuguang Duan) 96 Nov 01, 2022
Age Progression/Regression by Conditional Adversarial Autoencoder

Age Progression/Regression by Conditional Adversarial Autoencoder (CAAE) TensorFlow implementation of the algorithm in the paper Age Progression/Regre

Zhifei Zhang 603 Dec 22, 2022
Voice assistant - Voice assistant with python

🌐 Python Voice Assistant 🌵 - User's greeting 🌵 - Writing tasks to todo-list ?

PythonToday 10 Dec 26, 2022
Implementation of paper "Self-supervised Learning on Graphs:Deep Insights and New Directions"

SelfTask-GNN A PyTorch implementation of "Self-supervised Learning on Graphs: Deep Insights and New Directions". [paper] In this paper, we first deepe

Wei Jin 85 Oct 13, 2022
The 2nd place solution of 2021 google landmark retrieval on kaggle.

Leaderboard, taxonomy, and curated list of few-shot object detection papers.

229 Dec 13, 2022
The repo of Feedback Networks, CVPR17

Feedback Networks http://feedbacknet.stanford.edu/ Paper: Feedback Networks, CVPR 2017. Amir R. Zamir*,Te-Lin Wu*, Lin Sun, William B. Shen, Bertram E

Stanford Vision and Learning Lab 87 Nov 19, 2022
Official PyTorch implementation of "Contrastive Learning from Extremely Augmented Skeleton Sequences for Self-supervised Action Recognition" in AAAI2022.

AimCLR This is an official PyTorch implementation of "Contrastive Learning from Extremely Augmented Skeleton Sequences for Self-supervised Action Reco

Gty 44 Dec 17, 2022
A hybrid framework (neural mass model + ML) for SC-to-FC prediction

The current workflow simulates brain functional connectivity (FC) from structural connectivity (SC) with a neural mass model. Gradient descent is applied to optimize the parameters in the neural mass

Yilin Liu 1 Jan 26, 2022
Adaptive, interpretable wavelets across domains (NeurIPS 2021)

Adaptive wavelets Wavelets which adapt given data (and optionally a pre-trained model). This yields models which are faster, more compressible, and mo

Yu Group 50 Dec 16, 2022
PyTorch implementation of the ExORL: Exploratory Data for Offline Reinforcement Learning

ExORL: Exploratory Data for Offline Reinforcement Learning This is an original PyTorch implementation of the ExORL framework from Don't Change the Alg

Denis Yarats 52 Jan 01, 2023
Robbing the FED: Directly Obtaining Private Data in Federated Learning with Modified Models

Robbing the FED: Directly Obtaining Private Data in Federated Learning with Modified Models This repo contains a barebones implementation for the atta

16 Dec 04, 2022
Learning Optical Flow from a Few Matches (CVPR 2021)

Learning Optical Flow from a Few Matches This repository contains the source code for our paper: Learning Optical Flow from a Few Matches CVPR 2021 Sh

Shihao Jiang (Zac) 159 Dec 16, 2022
Facilitating Database Tuning with Hyper-ParameterOptimization: A Comprehensive Experimental Evaluation

A Comprehensive Experimental Evaluation for Database Configuration Tuning This is the source code to the paper "Facilitating Database Tuning with Hype

DAIR Lab 9 Oct 29, 2022
Official page of Struct-MDC (RA-L'22 with IROS'22 option); Depth completion from Visual-SLAM using point & line features

Struct-MDC (click the above buttons for redirection!) Official page of "Struct-MDC: Mesh-Refined Unsupervised Depth Completion Leveraging Structural R

Urban Robotics Lab. @ KAIST 37 Dec 22, 2022
Instantaneous Motion Generation for Robots and Machines.

Ruckig Instantaneous Motion Generation for Robots and Machines. Ruckig generates trajectories on-the-fly, allowing robots and machines to react instan

Berscheid 374 Dec 23, 2022
A curated list of awesome resources related to Semantic Search🔎 and Semantic Similarity tasks.

A curated list of awesome resources related to Semantic Search🔎 and Semantic Similarity tasks.

224 Jan 04, 2023
Captcha-tensorflow - Image Captcha Solving Using TensorFlow and CNN Model. Accuracy 90%+

Captcha Solving Using TensorFlow Introduction Solve captcha using TensorFlow. Learn CNN and TensorFlow by a practical project. Follow the steps, run t

Jackon Yang 869 Jan 06, 2023
NNR conformation conditional and global probabilities estimation and analysis in peptides or proteins fragments

NNR and global probabilities estimation and analysis in peptides or protein fragments This module calculates global and NNR conformation dependent pro

0 Jul 15, 2021